As far as I understood, you are trying to make some kind of a sound level detector, which will let you detect if there is a sound with a certain volume or not. You can do this with minor changes to the schematic you have. But before that, you should understand the circuit.
Let's break that circuit down. First of all the part with the microphone.
R1 is for supplying power that is needed by the microphone and this is called biasing the microphone. A microphone generates an AC voltage, which is sometimes negative and sometimes positive and it changes most of the time. Think of a sine wave. But remember, we had some biasing to it which is a DC voltage. We have to take that out and give only the AC voltage to the amplifier. And doing this is easy with a simple, single capacitor. A capacitor does not let the DC to pass, but lets AC pass easily. We have blocked the DC portion of the voltage on the electret microphone.
Now, let's look at the amplifier itself. Imagine that there is nothing else but the below schematic:
In this configuration, the transistor is biased to be in the linear region. It is in the edge of being turned ON or turned OFF, but it is neither of it. If it was fully ON, it would be saturated. If it was fully OFF, it would be not conducting at all. But it is in the middle, which is called the linear region.
When it is configured like that, if you touch (not literally) to the base of it, creating a small change, the output will be changing largely. This is what amplification called. You can beg Google for more detailed information.
What if we combine the two circuits mentioned above. A biased electret microphone with a capacitor will output small changes with respect to sound. The transistor will amplify these small changes so they can be viewed easily:
Notice that I have changed C1 to 1uF. You can use values up to 100uF. You will probably need electrolytic capacitors. Also, notice that there is no more an output capacitor. This means that you will have an output voltage somewhere between 0 and 5 V, depending on the sound level. If you have an oscilloscope, view the waveform on the output. If you do not, try lighting an LED if the analog read is higher than, for example, 750. Experiment with different values than 750, then report me the results.
Here's the circuit you linked to with a couple of red circles on it: -
Check that capacitor C1 isn't somehow leaking some DC current through to the -Vin pin.
Also check that R4 is fitted correctly and you can measure the same voltages on each of it's pins as you do on the op-amp pins. R4 could be broken - can you measure it with a meter?
Measure that copper tracks are fine between R4 and the op-amp.
If necessary lift C1 from the circuit to check that -Vin and +Vin become the same level.
The OPA345 is unquestionable a good device for this application if you don't care too much about noise. The AD8606 does the same but will produce less noise.
Best Answer
The DC currents through R1 and R5 are flowing through R3, causing the virtual ground to increase in voltage. According to the OP the gain is working correctly now.